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SVision: a deep learning approach to resolve complex structural variants

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  1. Article

    Open Access

    Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution

    Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet ...

    Qing Meng, Zhanling **e, Hongyan Xu, **g Guo, Qingqing Peng, Yanyan Li in BMC Genomics (2024)

  2. Article

    Open Access

    De novo and somatic structural variant discovery with SVision-pro

    Long-read-based de novo and somatic structural variant (SV) discovery remains challenging, necessitating genomic comparison between samples. We developed SVision-pro, a neural-network-based instance segmentati...

    Songbo Wang, Jiadong Lin, Peng Jia, Tun Xu, **ujuan Li in Nature Biotechnology (2024)

  3. Article

    Open Access

    Integrated analysis of the ubiquitination mechanism reveals the specific signatures of tissue and cancer

    Ubiquitination controls almost all cellular processes. The dysregulation of ubiquitination signals is closely associated with the initiation and progression of multiple diseases. However, there is little compr...

    Deyu Long, Ruiqi Zhang, Changjian Du, Jiapei Tong, Yu Ni, Yaqi Zhou in BMC Genomics (2023)

  4. Article

    CD-NTase family member MB21D2 promotes cGAS-mediated antiviral and antitumor immunity

    cGAS/DncV-like nucleotidyltransferase (CD-NTase) family members are immune sensors that synthesize diverse nucleotide signals to initiate antiviral response in bacteria and animals. As a founding member of CD-...

    Hansen Liu, Zhenzhen Yan, Deyu Zhu, Haiyan Xu, Feng Liu in Cell Death & Differentiation (2023)

  5. Article

    Open Access

    Hepatocyte growth factor-mediated apoptosis mechanisms of cytotoxic CD8+ T cells in normal and cirrhotic livers

    Intrahepatic stem/progenitor cells and cytotoxic CD8+ T cells (CD8+ T cells) in the cirrhotic liver undergo apoptosis, which potentially facilitates progression to cancer. Here, we report that hepatocyte growth f...

    Quanyu Chen, Min Yan, Heng Lin, Jiejuan Lai, Zhiqing Yang, Deyu Hu in Cell Death Discovery (2023)

  6. Article

    Open Access

    Correction to: DC-SIGN–LEF1/TCF1–miR-185 feedback loop promotes colorectal cancer invasion and metastasis

    A Correction to this paper has been published: https://doi.org/10.1038/s41418-021-00736-9

    Menglang Yuan, **nsheng Zhang, **gbo Zhang, Keyong Wang in Cell Death & Differentiation (2022)

  7. Article

    A glucose-like metabolite deficient in diabetes inhibits cellular entry of SARS-CoV-2

    The severity and mortality of COVID-19 are associated with pre-existing medical comorbidities such as diabetes mellitus. However, the underlying causes for increased susceptibility to viral infection in patien...

    Liangqin Tong, Min Li, Shisong Fang, Enhao Ma, ** Yu in Nature Metabolism (2022)

  8. Article

    Open Access

    Ferroptosis-associated DNA methylation signature predicts overall survival in patients with head and neck squamous cell carcinoma

    Head and neck squamous cell carcinoma (HNSCC) is a common cancer characterized by late diagnosis and poor prognosis. The aim of this study was to identify a novel ferroptosis-related DNA methylation signature ...

    Yuanyuan Xu, Min Hong, Deyu Kong, Jun Deng, Zhaoming Zhong, ** Liang in BMC Genomics (2022)

  9. Article

    Open Access

    Avibactam potentiated the activity of both ceftazidime and aztreonam against S. maltophilia clinical isolates in vitro

    Treatment options for Stenotrophomonas maltophilia (S. maltophilia) infections were limited. We assessed the efficacy of ceftazidime (CAZ), ceftazidime-avibactam (CAZ-AVI), aztreonam (ATM), and aztreonam-avibacta...

    Qiuxia Lin, Hua Zou, **an Chen, Menglu Wu, Deyu Ma, Hanbing Yu in BMC Microbiology (2021)

  10. Article

    Open Access

    Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie)

    Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the ...

    Jiyong **e, Jiaqi Li, Yucheng Jie, Deyu **e, Di Yang, Huazhong Shi in BMC Genomics (2020)

  11. Article

    Open Access

    DC-SIGN–LEF1/TCF1–miR-185 feedback loop promotes colorectal cancer invasion and metastasis

    DC-SIGN is previously focused on its physiologic and pathophysiologic roles in immune cells. Little is known about whether DC-SIGN is expressed in malignant epithelial cells and how DC-SIGN participates in tum...

    Menglang Yuan, **nsheng Zhang, **gbo Zhang, Keyong Wang in Cell Death & Differentiation (2020)

  12. Article

    Open Access

    MicroRNA-153-3p enhances cell radiosensitivity by targeting BCL2 in human glioma

    Glioma is the most prevalent malignant tumor in human central nervous systems. Recently, the development of resistance to radiotherapy in glioma patients markedly vitiates the therapy outcome. MiR-153-3p has b...

    Deyu Sun, Yi Mu, Haozhe Piao in Biological Research (2018)

  13. Article

    PslG, a self-produced glycosyl hydrolase, triggers biofilm disassembly by disrupting exopolysaccharide matrix

    Biofilms are surface-associated communities of microorganism embedded in extracellular matrix. Exopolysaccharide is a critical component in the extracellular matrix that maintains biofilm architecture and prot...

    Shan Yu, Tiantian Su, Huijun Wu, Shiheng Liu, Di Wang, Tianhu Zhao in Cell Research (2015)

  14. Article

    Open Access

    Ubiquitin-specific protease 22 is a deubiquitinase of CCNB1

    The elevated level of CCNB1 indicates more aggressive cancer and poor prognosis. However, the factors that cause CCNB1 upregulation remain enigmatic. Herein, we identify USP22 as a CCNB1 interactor and discove...

    Zhenghong Lin, Can Tan, Quan Qiu, Sinyi Kong, Heeyoung Yang, Fang Zhao in Cell Discovery (2015)

  15. Article

    Open Access

    A novel ER–microtubule-binding protein, ERLIN2, stabilizes Cyclin B1 and regulates cell cycle progression

    The gene encoding endoplasmic reticulum (ER) lipid raft-associated protein 2 (ERLIN2) is amplified in human breast cancers. ERLIN2 gene mutations were also found to be associated with human childhood progressive ...

    Xuebao Zhang, Juan Cai, Ze Zheng, Lisa Polin, Zhenghong Lin in Cell Discovery (2015)

  16. Article

    Open Access

    Determination of delay time in individual transfer function for central aortic pressure reconstruction

    In previous research, time-delay (Δt) was a more important parameter than the reflection coefficient in the individual transfer function of central aortic pressure reconstruction. The Δt can be obtained by electr...

    DanYang Yu, HaiYang **ang, DeYu Li, YuQi Wang, MengSun Yu in Science China Life Sciences (2014)

  17. Article

    Open Access

    Relationship between triphasic mechanical properties of articular cartilage and osteoarthritic grade

    The purpose of this study was to explore the triphasic mechanical properties of osteoarthritic cartilage with different pathological grades. First, samples of cartilage from rabbits with different stages of os...

    HaiJun Niu, ChengRui Liu, Ang Li, Qing Wang, Yue**ang Wang in Science China Life Sciences (2012)

  18. Article

    Open Access

    Ultrasound speed and attenuation in progressive trypsin digested articular cartilage

    Subtle changes of articular cartilage (AC) can lead to tissue degeneration and even osteoarthritis (OA). The early degeneration of AC is closely related to a change in proteoglycans (PG) content. The observati...

    HaiJun Niu, LiFeng Li, Feng Sun, Yan Yan, Yue**ang Wang in Science China Life Sciences (2011)

  19. Article

    Open Access

    Vesicle-independent extracellular release of a proinflammatory outer membrane lipoprotein in free-soluble form

    Aggregatibacter actinomycetemcomitans is an oral bacterium associated with aggressively progressing periodontitis. Extracellular release of bacterial outer membrane proteins has been suggested to mainly occur via...

    Maribasappa Karched, Riikka Ihalin, Kjell Eneslätt, Deyu Zhong in BMC Microbiology (2008)

  20. Article

    Whole-virus Vaccine Development by Continuous Culture on a Complementing Host

    We have evaluated an adaptive strategy for generating whole-virus vaccines using a bacteriophage model. Wildtype phage T7 was cultivated in a two-stage continuous stirred-tank reactor (CSTR) utilizing a recomb...

    Deyu Kong, John Yin in Bio/Technology (1995)